Align Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized)
to candidate SMc00086 SMc00086 diheme cytochrome C-type signal peptide protein
Query= SwissProt::O34215 (441 letters) >FitnessBrowser__Smeli:SMc00086 Length = 304 Score = 152 bits (384), Expect = 1e-41 Identities = 92/265 (34%), Positives = 136/265 (51%), Gaps = 14/265 (5%) Query: 31 GEYLARAGDCVACHSVKGGQP-----FAGGLPMATPIGTIYSTNITPDKTTGIGDYSYDD 85 GE + AG CV+CHS G + GG + +P GT Y NI+PD+T GIG+++ + Sbjct: 48 GEQIFWAGGCVSCHSAPGAKDDQRLVLTGGRTLKSPFGTFYPPNISPDETVGIGNWTLAE 107 Query: 86 FQKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKALYAYFMHGVAPVAQANKDSDIPWPL 145 F A+ GV K+G+ LYP+ PY SY ++ +D+ L+ FM + + A D+ +P Sbjct: 108 FGDAMTRGVGKDGEHLYPSFPYGSYIRMTAKDVNDLWG-FMQTLPKSSNATPPHDLAFPY 166 Query: 146 SMRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYLVEGLGHCGACHTPRSITMQEKALS 205 ++R L W+ ++ D Q D LARG+YLVEG GHCG CHTPR AL Sbjct: 167 NVRLALGAWKLLYLSDEPRTQ-VNTADTKLARGQYLVEGPGHCGECHTPRD------ALG 219 Query: 206 NDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSEDDLRQFLRYGRNDHTAAFGGMTDV 265 +L+G+ P ++ ++ +G WS D+ +L G GG Sbjct: 220 GFEEDRWLAGAPNPEGEGRIPDITPSSK-SIGDWSASDIASYLETGFTPDFDTVGGSMVE 278 Query: 266 VEHSLQHLSDDDITAIARYLKSLGA 290 V+ ++ L D AIA YLK+L A Sbjct: 279 VQKNMAELPASDRDAIAAYLKALPA 303 Score = 28.5 bits (62), Expect = 3e-04 Identities = 26/119 (21%), Positives = 44/119 (36%), Gaps = 23/119 (19%) Query: 124 YFMHGVAPVAQANKDSDIPWPLSM--RWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYL 181 Y + G+ + A + + W L+ RW A W G+ PD LA G + Sbjct: 7 YLLSGLVLLVVAG--ASLAWWLTKPDRWDAAHWEGLGGPD-------------LANGEQI 51 Query: 182 VEGLGHCGACHTPRSITMQEKALSNDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWS 240 G C +CH+ ++ + G +P + N+ D G+G W+ Sbjct: 52 F-WAGGCVSCHSAPGAKDDQRLVLTGG-----RTLKSPFGTFYPPNISPDETVGIGNWT 104 Lambda K H 0.317 0.133 0.409 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 488 Number of extensions: 37 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 441 Length of database: 304 Length adjustment: 30 Effective length of query: 411 Effective length of database: 274 Effective search space: 112614 Effective search space used: 112614 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory